This is just my opinion. I can totally relate to HE being upset and crying b/c she is torn between her heart and her head.
Yes, she probably still has feelings for SM. However, he had broken things off with her weeks before, and had not contacted her since.
Emotionally, she was probably still recovering from this - she was doing better because of distance from the situation.
if it were me, I would be hurt and still angry from being treated that way. If the person that had treated me that way called and said "I want to be with you and see you, I've left my wife", I would have all kinds of conflicting feelings.
The history of her relationship with him, being that he was married, had 3 kids with his wife, his wife found out about the relationship and was sending threatening texts, and whatever else was sent, was volatile.
If it were me, even though I really did want to be with him (heart), I can guarantee you that I would know that being with him was not in my best interest (head). That would upset me. Even if he had said he was leaving his wife, I would wonder if he would follow through considering past history of their relationship. Maybe SM had told HE that he was leaving TM, or wanted to leave TM at some other point in their relationship, i dunno.
So, for me, that is why I can totally believe HE's version of the conversation. I can relate to that feeling of being torn, and have felt it before. Again, this is just my opinion.